The bottom line is that science and technology exist in a social, economic, and political milieu, and it is perfectly valid to guide and regulate them according to this milieu. Many potential lines in medical research are forbidden by ethical concerns--certain types of human or animal testing, stem-cell work, etc. Some societies have decided to limit or strictly circumscribe the use and study of nuclear energy. Certain industrial technologies that would negatively impact workers or small producers are discouraged by legislation (for instance Colombia's policy of reserving panela production to small farmers as a way of promoting rural livelihoods and preventing mass banditry and insurgency of displaced farmers). We should all probably put strict controls on self-replicating technologies of global impact, such as nanotechnology or geoengineering.

I would argue that, because of its self-replicating and inevitable potential of transgenes to spread throughout the entire gene pool for a given species, genetic engineering should be another such technology that we strictly regulate. Just as bison conservationists try to maintain at least a reserve population of "pure" bison, that is bison that have never been crossed with domestic cattle genes, society should strive to maintain plant and animal populations free of transgenes. There's nothing inherently bad about the cattle genes, and in fact domestic cattle are very close genetically to bison (that's why they can interbreed). But I think most people can agree on the inherent value of purity in the natural world--full-blood bison, natural areas free from invasives, seas without man-made chemicals, food without petroleum-derived additives.

You could argue that everything under the sun is in fact natural, and thus that such emphasis on "purity" is misplaced. A cow is not inherently better or worse than a bison. One plant species is not inherently superior to another. Indeed, even man-made plastics or anything else extracted from petroleum is ultimately "natural", in that petroleum is ultimately derived from plants and animals that lived millions of years ago. But I think that such justifications would ring hollow to most people, and reasonably so. We all know the difference between a wild animal population and a domesticated species, or an intact ecosystem versus one degraded by invasives or synthetic chemicals.

On this basis I would argue for keeping transgenes out of our natural and managed ecosystems, to the extent possible. Having a Bt gene present in native Mesoamerican corn and its relatives will not kill any people, and it might not even alter the local insect populations that much. But something will be lost, just as it would be if there were some heavy metal or organic solvent or invasive plant added by humankind to those Mesoamerican ecosystems.